Document Detail

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
MedLine Citation:
PMID:  15210349     Owner:  NLM     Status:  MEDLINE    
2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.
Noriyasu Ohshima; Eiji Inagaki; Kiyonori Yasuike; Koji Takio; Tahir H Tahirov
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of molecular biology     Volume:  340     ISSN:  0022-2836     ISO Abbreviation:  J. Mol. Biol.     Publication Date:  2004 Jul 
Date Detail:
Created Date:  2004-06-22     Completed Date:  2004-08-09     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  2985088R     Medline TA:  J Mol Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  477-89     Citation Subset:  IM    
Copyright Information:
Copyright 2004 Elsevier Ltd.
Highthroughput Factory, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.
Data Bank Information
Bank Name/Acc. No.:
PDB/1V19;  1V1A;  1V1B;  1V1S
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MeSH Terms
Adenosine Triphosphate / metabolism
Amino Acid Sequence
Models, Molecular
Molecular Sequence Data
Phosphotransferases (Alcohol Group Acceptor) / chemistry,  metabolism*
Protein Conformation
Protein Folding
Sequence Homology, Amino Acid
Substrate Specificity
Thermus thermophilus / enzymology*
Reg. No./Substance:
56-65-5/Adenosine Triphosphate; EC 2.7.1.-/Phosphotransferases (Alcohol Group Acceptor); EC

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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